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RiboMethSeq is an RNAseq-based approach to analyze 2’O-ribose methylation (2’Ome).

rRMSAnalyzer is an R package that provides a set of easy-to-use functions to evaluate 2’Ome levels by computing C-scores from RiboMethSeq read end counts as input.

Available features (version 3):

  • C-score computation
  • Batch effect adjustment with CombatSeq
  • Different visualizations to compare samples or sites
  • Include a table of annotated human rRNA sites
  • Export computed C-scores into a dataframe
  • Three novel functions to compute automatically reports (QC report and 2 analytic reports dedicated to 2’Ome profiles and site-by-site change in 2’Ome)

Note: We have also developed a dedicated Nextflow pipeline (ribomethseq-nf) to process the data from sequencing output (fastq files) to useful raw data for rRMSAnalyzer (read end counts).

Installation

The latest version of rRMSAnalyzer package can be installed from Github with:

library(devtools)
devtools::install_github("RibosomeCRCL/rRMSAnalyzer")

Usage

library(rRMSAnalyzer)

ribo <- load_ribodata(
              count_path = "/path/to/your/csvfiles/directory/",
              metadata = "path/to/metadata.csv",
              metadata_key = "filename",
              metadata_id = "samplename")

# Compute the C-score using different parameters,
# including calculation of the local coverage using the mean instead of the median
ribo <- compute_cscore(ribo, method = "mean")

# If necessary, adjust any technical biases using ComBat-Seq.
# Here, as an example, we use the "library" column in metadata.
ribo <- adjust_bias(ribo,"library")

# Plot a Principal Component Analysis (PCA) whose colors depend on the "condition" column in metadata
plot_pca(ribo,"condition")

Getting started

The “getting started” is available on our Github page: https://ribosomecrcl.github.io/rRMSAnalyzer/

A test dataset (ribo_toy) is included in the package.

Help, bug reports and suggestions

To report a bug or any suggestion to improve the package, please let us known by opening a new issue on: https://github.com/RibosomeCRCL/rRMSAnalyzer/issues

Acknowledgements

We would like to thank all our collaborators from Jean-Jacques Diaz Team and the Bioinformatic Platform Gilles Thomas for their advices and suggestions.

Funding

This project has been funded by the French Cancer Institute (INCa, PLBIO 2019-138 MARACAS, INCa_18375), the SIRIC Program (INCa-DGOS-Inserm_12563 LyRICAN), LabEX program (DEVweCan), the French association Ligue Nationale Contre le Cancer and Synergie Lyon Cancer Foundation.